FACS is a type of flow cytometry which allows the sorting of a heterogeneous mixture of cells into individual containers, one cell at a time, based upon the fluorescent and light scattering properties of each cell. It is useful characteristics of each cell. It is a useful technique, providing a fast and quantitative recording of individual fluorescent signals, as well as physically separating cells of interest.

The technique is of particular use in stem cell research. When cells are obtained from multicellular organisms, the DNA is naturally identical in each one. However, the proteins of each cell vary widely. Therefore, a method of separating cells based on their phenotype i.e. FACS is extremely useful. In addition, FACS allows us to see what percentage of the total cell population is expressing the protein of interest, and in what quantity.

The process involves the gentle forcing of cells through a fine, vibrating nozzle, one at a time. As the cells flow through, they are scanned by a laser. Some of the light is scattered, and this is used to count the cells. It also serves to measure the size of the cells.

Cell sub-populations can be separated by tagging with an antibodyconjugated with a fluorescent dye, targeted to a protein specific to those cells. When excited by the laser, the dye emits a particular wavelength of light, allowing the apparatus to identify and isolate the relevant cells.